I think the problem is, it's very configurable. To the point, some towered architect somewhere can make those decisions for you, about how you want to work, in your absence.

Out of the box, I'm not sure, I don't think I've ever seen it. If what I've seen is out-of-the-box, it's awful.

My experience is that some people don't like tracking their work, or figuring how to do it effectively and in a way that benefits not only themselves but their peers.

I get you're point about people fiddling with it, but that's usually because they never understood that JIRA is quite simple to begin with.